Molecular basis for functional diversity among microbial Nep1-like proteins

PLoS Pathog. 2019 Sep 3;15(9):e1007951. doi: 10.1371/journal.ppat.1007951. eCollection 2019 Sep.

Abstract

Necrosis and ethylene-inducing peptide 1 (Nep1)-like proteins (NLPs) are secreted by several phytopathogenic microorganisms. They trigger necrosis in various eudicot plants upon binding to plant sphingolipid glycosylinositol phosphorylceramides (GIPC). Interestingly, HaNLP3 from the obligate biotroph oomycete Hyaloperonospora arabidopsidis does not induce necrosis. We determined the crystal structure of HaNLP3 and showed that it adopts the NLP fold. However, the conformations of the loops surrounding the GIPC headgroup-binding cavity differ from those of cytotoxic Pythium aphanidermatum NLPPya. Essential dynamics extracted from μs-long molecular dynamics (MD) simulations reveals a limited conformational plasticity of the GIPC-binding cavity in HaNLP3 relative to toxic NLPs. This likely precludes HaNLP3 binding to GIPCs, which is the underlying reason for the lack of toxicity. This study reveals that mutations at key protein regions cause a switch between non-toxic and toxic phenotypes within the same protein scaffold. Altogether, these data provide evidence that protein flexibility is a distinguishing trait of toxic NLPs and highlight structural determinants for a potential functional diversification of non-toxic NLPs utilized by biotrophic plant pathogens.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Ethylenes / metabolism
  • Necrosis / metabolism
  • Oomycetes / genetics*
  • Oomycetes / metabolism*
  • Peptides / metabolism
  • Peronospora / genetics
  • Plant Diseases / parasitology*
  • Proteins / metabolism
  • Ribosomal Proteins / genetics
  • Ribosomal Proteins / metabolism
  • Saccharomyces cerevisiae Proteins / genetics
  • Saccharomyces cerevisiae Proteins / metabolism

Substances

  • EMG1 protein, S cerevisiae
  • Ethylenes
  • Peptides
  • Proteins
  • Ribosomal Proteins
  • Saccharomyces cerevisiae Proteins
  • ethylene

Grants and funding

This work was supported by the Slovenian Research Agency (P1-0391, J1-7515) and Seventh Framework Program BioStructX N°283570. JB thanks AREA Science Park for the TALENTS3 Fellowship Program. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.